Repitools: Epigenomic tools

Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

Author
Mark Robinson <mark.robinson@imls.uzh.ch>, Dario Strbenac <dario.strbenac@sydney.edu.au>, Aaron Statham <a.statham@garvan.org.au>, Andrea Riebler <andrea.riebler@math.ntnu.no>
Date of publication
None
Maintainer
Mark Robinson <mark.robinson@imls.uzh.ch>
License
LGPL (>= 2)
Version
1.20.0

View on Bioconductor

Man pages

abcdDNA
A wrapper for fitting the offset-adjusted ABCD-DNA GLM
absoluteCN
Calculate and Segment Absolute Copy Number from Sequencing...
AdjustedCopyEstimate-class
Container for results of GC adjusted copy number estimation.
AffymetrixCdfFile-class
Placeholder For AffymetrixCdfFile Documentation
AffymetrixCelSet-class
Placeholder For AffymetrixCelSet Documentation
annoDF2GR
Convert a 'data.frame' to a 'GRanges'.
annoGR2DF
Convert an annotated 'GRanges' to a 'data.frame'.
annotationBlocksCounts
Counts the number of sequencing reads within supplied genomic...
annotationBlocksLookup
Forms a mapping between probe locations and chromosomal...
annotationCounts
Counts the number of sequencing reads surrounding supplied...
annotationLookup
Forms a mapping between probes on a tiling array and windows...
BAM2GRanges
Read in a (list of) BAM file(s) into a GRanges(List) object.
BayMethList-class
Class '"BayMethList"'
binPlots
Create line plots of averaged signal across a promoter
blocksStats
Calculate statistics for regions in the genome
checkProbes
Check Probe Specificity for Some Regions
chr21genes
Positions of Genes on Human Chromosome 21
ChromaBlocks
A function to find areas of enrichment in sequencing data
ChromaResults-class
ChromaResults class
chromosomeCNplots
Plot copy number by chromosome
ClusteredScoresList-class
Container for coverage matrices with clustering results.
clusterPlots
Visualisation of tables of feature coverages.
CopyEstimate-class
Container for results of fold change copy number estimation.
cpgBoxPlots
Boxplots of intensity, binned by Cpg Density
cpgDensityCalc
Calculate CpG Density in a Window
cpgDensityPlot
Plot the distribution of sequencing reads CpG densities.
determineOffset
Function to determine the normalising offset f that accounts...
empBayes
Function to calculate prior parameters using empirical Bayes.
enrichmentCalc
Calculate sequencing enrichment
enrichmentPlot
Plot the distribution of sequencing enrichment.
expr
Vector of expression differences
FastQC-class
FastQC and associated classes
featureBlocks
Make windows for distances around a reference point.
featureScores
Get scores at regular sample points around genomic features.
findClusters
Find Clusters Epigenetically Modified Genes
GCadjustCopy
Calculate Absolute Copy Number from Sequencing Counts
GCAdjustParams-class
Container for parameters for mappability and GC content...
GCbiasPlots
Plot GC content vs. Read Counts Before Normalising, and GC...
gcContentCalc
Calculate The gcContent of a Region
genomeBlocks
Creates bins across a genome.
genQC
Plot Quality Checking Information for Sequencing Data
getProbePositionsDf
Translate Affymetrix probe information in a table.
getSampleOffsets
Calculates the sample-specific offsets, using the neutral...
hcRegions
Masking files for hg19
hyper
Gaussian hypergeometric function for vectorial arguments
loadPairFile
A routine to read Nimblegen tiling array intensities
loadSampleDirectory
A routine to read Nimblegen tiling array intensities
makeWindowLookupTable
Using the output of 'annotationLookup', create a tabular...
mappabilityCalc
Calculate The Mappability of a Region
MappabilitySource-class
Superclass for datatypes that can refer to genome mappability...
maskOut
Function to mask suspicious regions.
mergeReplicates
Merge GRanges that are of replicate experiments.
methylEst
Function to derive regional methylation estimates.
multiHeatmap
Superfigure plots
plotClusters
Plot Scores of Cluster Regions
plotQdnaByCN
Plotting the response of qDNA-seq data by CNV
processNDF
Reads in a Nimblegen microarray design file (NDF)
profilePlots
Create line plots of averaged signal across a promoter for...
QdnaData
A container for quantitative DNA sequencing data for ABCD-DNA...
regionStats
Find Regions of significance in microarray data
relativeCN
Calculate and Segment Relative Copy Number From Sequencing...
samplesList
Short Reads from Cancer and Normal
ScoresList-class
Container for 'featureScores()' output.
sequenceCalc
Find occurences of a DNA pattern
setCNVOffsets
Set the CNVOffsets of a 'QdnaData' object
summarizeScores
Subtract scores of different samples.
writeWig
Writes sequencing data out into wiggle files

Files in this package

Repitools/.Rinstignore
Repitools/DESCRIPTION
Repitools/NAMESPACE
Repitools/R
Repitools/R/BAM2GRanges.R
Repitools/R/ChromaBlocks.R
Repitools/R/FastQC-class.R
Repitools/R/GCadjustCopy.R
Repitools/R/GCbiasPlots.R
Repitools/R/abcdDNA.R
Repitools/R/absoluteCN.R
Repitools/R/annoDF2GR.R
Repitools/R/annoGR2DF.R
Repitools/R/annotationLookup.R
Repitools/R/binPlots.R
Repitools/R/blocksStats.R
Repitools/R/checkProbes.R
Repitools/R/chromosomeCNplots.R
Repitools/R/classes.R
Repitools/R/clusterPlots.R
Repitools/R/cpgBoxplots.R
Repitools/R/cpgDensityCalc.R
Repitools/R/cpgDensityPlot.R
Repitools/R/determineOffset.R
Repitools/R/empBayes.R
Repitools/R/enrichmentCalc.R
Repitools/R/enrichmentPlot.R
Repitools/R/featureBlocks.R
Repitools/R/featureScores.R
Repitools/R/findClusters.R
Repitools/R/gcContentCalc.R
Repitools/R/genQC.R
Repitools/R/genomeBlocks.R
Repitools/R/getProbePositionsDf.R
Repitools/R/hyper.R
Repitools/R/makeWindowLookup.R
Repitools/R/mappabilityCalc.R
Repitools/R/maskOut.R
Repitools/R/mergeReplicates.R
Repitools/R/methylEst.R
Repitools/R/multiHeatmap.R
Repitools/R/plotClusters.R
Repitools/R/processNimblegenArrays.R
Repitools/R/profilePlots.R
Repitools/R/regionStats.R
Repitools/R/relativeCN.R
Repitools/R/sequenceCalc.R
Repitools/R/summarizeScores.R
Repitools/R/utils.R
Repitools/R/writeWig.R
Repitools/build
Repitools/build/vignette.rds
Repitools/data
Repitools/data/chr21genes.csv
Repitools/data/datalist
Repitools/data/expr.RData
Repitools/data/hcRegions.RData
Repitools/data/samplesList.RData
Repitools/inst
Repitools/inst/CITATION
Repitools/inst/doc
Repitools/inst/doc/Repitools_vignette.R
Repitools/inst/doc/Repitools_vignette.Rnw
Repitools/inst/doc/Repitools_vignette.pdf
Repitools/inst/examples
Repitools/inst/examples/annotationCounts_seq.R
Repitools/inst/examples/binPlots_affy.R
Repitools/inst/examples/binPlots_seq.R
Repitools/inst/examples/blockStats_affy.R
Repitools/inst/examples/clusterPlots_seq.R
Repitools/inst/examples/cpgDensityPlot_seq.R
Repitools/inst/examples/enrichmentPlot_seq.R
Repitools/inst/examples/featureScores_array.R
Repitools/inst/examples/featureScores_seq.R
Repitools/inst/examples/findClusters_dataframe.R
Repitools/inst/examples/mergeReplicates_seq.R
Repitools/inst/examples/regionStats_affy.R
Repitools/man
Repitools/man/AdjustedCopyEstimate-class.Rd
Repitools/man/AffymetrixCdfFile-class.Rd
Repitools/man/AffymetrixCelSet-class.Rd
Repitools/man/BAM2GRanges.Rd
Repitools/man/BayMethList-class.Rd
Repitools/man/ChromaBlocks.Rd
Repitools/man/ChromaResults-class.Rd
Repitools/man/ClusteredScoresList-class.Rd
Repitools/man/CopyEstimate-class.Rd
Repitools/man/FastQC-class.Rd
Repitools/man/GCAdjustParams-class.Rd
Repitools/man/GCadjustCopy.Rd
Repitools/man/GCbiasPlots.Rd
Repitools/man/MappabilitySource-class.Rd
Repitools/man/QdnaData.Rd
Repitools/man/ScoresList-class.Rd
Repitools/man/abcdDNA.Rd
Repitools/man/absoluteCN.Rd
Repitools/man/annoDF2GR.Rd
Repitools/man/annoGR2DF.Rd
Repitools/man/annotationBlocksCounts.Rd
Repitools/man/annotationBlocksLookup.Rd
Repitools/man/annotationCounts.Rd
Repitools/man/annotationLookup.Rd
Repitools/man/binPlots.Rd
Repitools/man/blocksStats.Rd
Repitools/man/checkProbes.Rd
Repitools/man/chr21genes.Rd
Repitools/man/chromosomeCNplots.Rd
Repitools/man/clusterPlots.Rd
Repitools/man/cpgBoxPlots.Rd
Repitools/man/cpgDensityCalc.Rd
Repitools/man/cpgDensityPlot.Rd
Repitools/man/determineOffset.Rd
Repitools/man/empBayes.Rd
Repitools/man/enrichmentCalc.Rd
Repitools/man/enrichmentPlot.Rd
Repitools/man/expr.Rd
Repitools/man/featureBlocks.Rd
Repitools/man/featureScores.Rd
Repitools/man/findClusters.Rd
Repitools/man/gcContentCalc.Rd
Repitools/man/genQC.Rd
Repitools/man/genomeBlocks.Rd
Repitools/man/getProbePositionsDf.Rd
Repitools/man/getSampleOffsets.Rd
Repitools/man/hcRegions.Rd
Repitools/man/hyper.Rd
Repitools/man/loadPairFile.Rd
Repitools/man/loadSampleDirectory.Rd
Repitools/man/makeWindowLookupTable.Rd
Repitools/man/mappabilityCalc.Rd
Repitools/man/maskOut.Rd
Repitools/man/mergeReplicates.Rd
Repitools/man/methylEst.Rd
Repitools/man/multiHeatmap.Rd
Repitools/man/plotClusters.Rd
Repitools/man/plotQdnaByCN.Rd
Repitools/man/processNDF.Rd
Repitools/man/profilePlots.Rd
Repitools/man/regionStats.Rd
Repitools/man/relativeCN.Rd
Repitools/man/samplesList.Rd
Repitools/man/sequenceCalc.Rd
Repitools/man/setCNVOffsets.Rd
Repitools/man/summarizeScores.Rd
Repitools/man/writeWig.Rd
Repitools/src
Repitools/src/Makevars
Repitools/src/Makevars.win
Repitools/src/Rexchange.h
Repitools/src/const.c
Repitools/src/hyp2f1.c
Repitools/src/mconf.h
Repitools/src/mtherr.c
Repitools/tests
Repitools/tests/tests.R
Repitools/vignettes
Repitools/vignettes/Repitools_vignette.Rnw
Repitools/vignettes/analyses1.tex
Repitools/vignettes/analyses2.tex
Repitools/vignettes/clusterPlot.png
Repitools/vignettes/datasets.tex
Repitools/vignettes/qc-cpgPlot.pdf
Repitools/vignettes/qc-enrPlot.pdf
Repitools/vignettes/qc.tex
Repitools/vignettes/readme.txt
Repitools/vignettes/rock1.png
Repitools/vignettes/sInfo.tex
Repitools/vignettes/utilities.tex
Repitools/vignettes/visualisations-binPlotsHeatmap.pdf
Repitools/vignettes/visualisations-binPlotsLine.pdf
Repitools/vignettes/visualisations-cluPlots3.pdf
Repitools/vignettes/visualisations-profPlots.pdf
Repitools/vignettes/visualisations.tex